The Argentine set a 1m46.249s after overcoming earlier track limits issues to take the front spot for Sunday’s feature race, setting a time to go top which then withstood an effort from Trident's Roman Stanek.
Colapinto was still yet to set a representative lap with 10 minutes to go after his previous quick run was deleted for exceeding track limits, with stewards waving the black and white flag as a warning.
As the pack re-emerged in the second half of the session for a second round of runs, led out by Williams junior and Aston Martin Autosport BRDC Award winner Zak O’Sullivan, the times tumbled with Colapinto managing to snatch the top spot with a 1m46.249s.
Roman Stanek took second place for 2021 teams’ champions Trident having led this morning’s practice session.
Rookie Kush Maini finished in third for MP Motorsport, but will have to start from the pitlane for both races after missing the weighbridge.
The penalty promotes rookie Gregoire Saucy, driving for ART Grand Prix, to third place.
Stanek bettered his previous time to set a 1m46.314s, putting him up into second, with Saucy in third 0.1s behind him, before a late dash from Maini bumped him down into fourth.
Saucy thus beat his ART team-mates Victor Martins and Juan Manuel Correa, who will line up for Sunday's race from fifth and sixth ahead of Barbadian rookie Zane Maloney.
Alexander Smolyar, who earned a late reprieve with MP Motorsport, was attempting to set a quick lap with less than a minute to go when he was interrupted by Ayrton Simmons, who was attempting to break away from the pack to start a fast lap.
It left the MP Motorsport driver, who is competing as an Authorised Neutral Driver under the FIA’s code of conduct for Russian drivers, to finish the session in eighth.
Newcomers Isack Hadjar and David Vidales completed the top 10.
The reverse-grid format for Saturday’s sprint race means O’Sullivan - who qualified 12th - will start at the front for Carlin, with fellow Briton Ollie Bearman in second for Prema Racing.
O’Sullivan made it out of the garage in front of the pack for the first set of runs, avoiding the traditional F3 qualifying traffic and becoming the first driver to set a representative lap with a 1m47.847s.
He was quickly knocked off the top spot as the rest of the grid put in their first quick laps, with Saucy ending up on top with a 1m46.978s as the first driver to break the 1m47s barrier.
Saucy continued to lead from Stanek and Caio Collet (MP Motorsport) at the halfway point, before Juan Manuel Correa (ART) put himself up from P12 into third with a 1m47.120s.
Smolyar then went fastest with a 1m46.642s, over 0.3s quicker than Saucy, but the blockage on his later lap from Simmons meant that he was unable to improve and fell down the order.
Just one second covered the top 18 after the first round of laps, with most drivers setting a time under 1m47s before heading into the pits around the halfway mark to change tyres.
Jak Crawford’s session was affected after a large amount of fluid leaked from the bottom of his Prema-run car while he was in the pits, although he managed to get back out on track with three minutes left on the clock.
Prema endured a difficult session, with Bearman the Italian squad's highest runner in 11th, with sophomore Arthur Leclerc only making 14th behind fellow second-year Caio Collet.
FIA F3 Bahrain qualifying results
| Cla | Driver | Team | Time | Gap |
|---|---|---|---|---|
| 1 |  Franco Colapinto | Van Amersfoort Racing | 1'46.249 | |
| 2 |  Roman Staněk |  Trident | 1'46.314 | 0.065 |
| 3 |  Kush Maini |  MP Motorsport | 1'46.322 | 0.073 |
| 4 |  Gregoire Saucy |  ART Grand Prix | 1'46.410 | 0.161 |
| 5 | Victor Martins | ART Grand Prix | 1'46.412 | 0.163 |
| 6 |  Juan Manuel Correa | ART Grand Prix | 1'46.600 | 0.351 |
| 7 | Zane Maloney | Trident | 1'46.622 | 0.373 |
| 8 |  Alexander Smolyar | MP Motorsport | 1'46.642 | 0.393 |
| 9 | Isack Hadjar |  HitechGP | 1'46.649 | 0.400 |
| 10 |  David Vidales | Campos Racing | 1'46.707 | 0.458 |
| 11 | Oliver Bearman | Prema Powerteam | 1'46.843 | 0.594 |
| 12 | Zak O'Sullivan | Carlin | 1'46.860 | 0.611 |
| 13 | Caio Collet | MP Motorsport | 1'46.945 | 0.696 |
| 14 | Arthur Leclerc | Prema Powerteam | 1'46.961 | 0.712 |
| 15 | Jonny Edgar | Trident | 1'47.025 | 0.776 |
| 16 | Rafael Villagómez | Van Amersfoort Racing | 1'47.086 | 0.837 |
| 17 | Reece Ushijima | Van Amersfoort Racing | 1'47.123 | 0.874 |
| 18 |  William Alatalo | Jenzer Motorsport | 1'47.159 | 0.910 |
| 19 | Kaylen Frederick | HitechGP | 1'47.207 | 0.958 |
| 20 | Pepe Martí | Campos Racing | 1'47.303 | 1.054 |
| 21 | Jak Crawford | Prema Powerteam | 1'47.371 | 1.122 |
| 22 | Ido Cohen | Jenzer Motorsport | 1'47.444 | 1.195 |
| 23 | Francesco Pizzi | Charouz Racing System | 1'47.499 | 1.250 |
| 24 | Brad Benavides | Carlin | 1'47.566 | 1.317 |
| 25 | Niko Kari | Jenzer Motorsport | 1'47.646 | 1.397 |
| 26 | Hunter Yeany | Campos Racing | 1'47.695 | 1.446 |
| 27 |  Nazim Azman | HitechGP | 1'47.702 | 1.453 |
| 28 | Enzo Trulli | Carlin | 1'47.796 | 1.547 |
| 29 | László Tóth | Charouz Racing System | 1'47.930 | 1.681 |
| 30 | Ayrton Simmons | Charouz Racing System | 1'48.009 | 1.760 |
| View full results | ||||
